That has always been the case though. For as long as I've use Linux as a desktop my $HOME directory has been littered with dot-files and folders. And as for Windows, things used to be so much worse. Since the UAC, Windows applications have been limited in where they can write to lest they annoy their users with frequent escalation prompts. Before the UAC developers often used to write files all over the place - it was a complete nightmare! In fact one of the primary purposes of the UAC - as I recall - was to reign developers in.

Even the UAC aside, on Windows you now have the application data directory and permissions on the registry which both take some reliance off random files dumped anywhere. Before then Windows was like the wild west. And we're not talking that long ago in terms of the history of Windows - Vista was released 11 years ago and it took a few years after that for developers to catch up.

Plus with the trend of moving everything to the web, you're getting fewer native applications which can write those random files in seemingly random locations (that's one of the few good things about the move to web applications in my personal opinion).

You'll always have problems with developers having their own opinions - that's inescapable. But things used to be so much worse.